Data used in this analysis

Specifically, in this experiment set, known experiment labels are:

General description

This report contains all the functional information that was requested by the options when functional_Hunter.R was executed. The functional categories can be:

+ Biological Process + Molecular Function + Cellular Component

All the functional categories are computed with ClusterProfiler and GO categories are computed also with TopGo.

Some sections will not show if there are not sinficative results. Each category is analysed using Over representation analysis (ORA) and Gene Set Analysis (GSEA). The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category. In the case of the GSEA method, all the genes are sorted by their fold-change and the algorithm scan which genes with similar fold-change shares a term of the selected functional category.

Statistics about input results obtained from DEGenes Expression Hunter are:

Gene_tag Genes
NOT_DEG 15848
POSSIBLE_DEG 255
PREVALENT_DEG 202

Top genes

Table of signifcant genes. Variables taken into account are being shown into table (except gene symbols/ID). Top of positive (30 items) and negative (26 items) are being shown in two different tables

Top positive

rownames input_IDs logFC_DESeq2 logFC_edgeR mean_logFCs SYMBOL
ENSG00000188921 ENSG00000188921 1.74197312456206 1.74228392512514 1.7421285248436 HACD4
ENSG00000258752 ENSG00000258752 1.75809108202292 1.75616819511886 1.75712963857089 NA
ENSG00000279530 ENSG00000279530 1.76290268387243 1.75301036860623 1.75795652623933 NA
ENSG00000258441 ENSG00000258441 1.7760825636795 1.77996997724824 1.77802627046387 LINC00641
ENSG00000249717 ENSG00000249717 1.78531787918718 1.7858588990575 1.78558838912234 PARM1-AS1
ENSG00000111371 ENSG00000111371 1.843689679795 1.83302778435901 1.83835873207701 SLC38A1
ENSG00000279166 ENSG00000279166 1.85115668380546 1.85517266528287 1.85316467454417 NA
ENSG00000213891 ENSG00000213891 1.87928368515626 1.87572539214103 1.87750453864865 RPL3P6
ENSG00000225313 ENSG00000225313 1.88902917007879 1.89286480631346 1.89094698819613 NA
ENSG00000134077 ENSG00000134077 1.89185588806699 1.89057064601236 1.89121326703968 THUMPD3
ENSG00000213625 ENSG00000213625 1.91082472104738 1.90810618133475 1.90946545119106 LEPROT
ENSG00000121454 ENSG00000121454 1.93380650924297 1.92831627738784 1.9310613933154 LHX4
ENSG00000225572 ENSG00000225572 2.06270994699042 2.05286311571601 2.05778653135322 DOCK4-AS1
ENSG00000073584 ENSG00000073584 2.25208183830399 2.23878012131638 2.24543097981018 SMARCE1
ENSG00000271533 ENSG00000271533 2.48977340153388 2.47565193004794 2.48271266579091 NA
ENSG00000235880 ENSG00000235880 4.28569421781593 3.99087231306659 4.13828326544126 NA
ENSG00000251586 ENSG00000251586 4.2855472216083 3.99680892781831 4.1411780747133 NA
ENSG00000232344 ENSG00000232344 4.35640415659817 4.0726854972581 4.21454482692813 LOC100419436
ENSG00000239503 ENSG00000239503 4.45300601599872 4.16126426346173 4.30713513973022 NA
ENSG00000279862 ENSG00000279862 4.15219467913303 4.88198035756045 4.51708751834674 NA
ENSG00000236434 ENSG00000236434 4.22897039377978 4.96204105093882 4.5955057223593 NA
ENSG00000228166 ENSG00000228166 4.4130961908377 5.13609335610494 4.77459477347132 MTND1P11
ENSG00000208028 ENSG00000208028 4.43080090566233 5.14219914778293 4.78650002672263 MIR616
ENSG00000274093 ENSG00000274093 4.46751039995011 5.19686640469241 4.83218840232126 NA
ENSG00000259950 ENSG00000259950 4.47434940757891 5.20193033004558 4.83813986881225 NA
ENSG00000257475 ENSG00000257475 4.49058063961706 5.21053708997933 4.8505588647982 NA
ENSG00000265625 ENSG00000265625 4.51258922011669 5.22035659802475 4.86647290907072 NA
ENSG00000253539 ENSG00000253539 4.66024587128113 5.38117831898838 5.02071209513475 NA
ENSG00000179038 ENSG00000179038 5.09426473364569 5.80355437865827 5.44890955615198 NA
ENSG00000085265 ENSG00000085265 5.41025559710872 6.11905544475849 5.76465552093361 FCN1

Top negative

rownames input_IDs logFC_DESeq2 logFC_edgeR mean_logFCs SYMBOL
ENSG00000188921 ENSG00000188921 1.74197312456206 1.74228392512514 1.7421285248436 HACD4
ENSG00000258752 ENSG00000258752 1.75809108202292 1.75616819511886 1.75712963857089 NA
ENSG00000279530 ENSG00000279530 1.76290268387243 1.75301036860623 1.75795652623933 NA
ENSG00000258441 ENSG00000258441 1.7760825636795 1.77996997724824 1.77802627046387 LINC00641
ENSG00000249717 ENSG00000249717 1.78531787918718 1.7858588990575 1.78558838912234 PARM1-AS1
ENSG00000111371 ENSG00000111371 1.843689679795 1.83302778435901 1.83835873207701 SLC38A1
ENSG00000279166 ENSG00000279166 1.85115668380546 1.85517266528287 1.85316467454417 NA
ENSG00000213891 ENSG00000213891 1.87928368515626 1.87572539214103 1.87750453864865 RPL3P6
ENSG00000225313 ENSG00000225313 1.88902917007879 1.89286480631346 1.89094698819613 NA
ENSG00000134077 ENSG00000134077 1.89185588806699 1.89057064601236 1.89121326703968 THUMPD3
ENSG00000213625 ENSG00000213625 1.91082472104738 1.90810618133475 1.90946545119106 LEPROT
ENSG00000121454 ENSG00000121454 1.93380650924297 1.92831627738784 1.9310613933154 LHX4
ENSG00000225572 ENSG00000225572 2.06270994699042 2.05286311571601 2.05778653135322 DOCK4-AS1
ENSG00000073584 ENSG00000073584 2.25208183830399 2.23878012131638 2.24543097981018 SMARCE1
ENSG00000271533 ENSG00000271533 2.48977340153388 2.47565193004794 2.48271266579091 NA
ENSG00000235880 ENSG00000235880 4.28569421781593 3.99087231306659 4.13828326544126 NA
ENSG00000251586 ENSG00000251586 4.2855472216083 3.99680892781831 4.1411780747133 NA
ENSG00000232344 ENSG00000232344 4.35640415659817 4.0726854972581 4.21454482692813 LOC100419436
ENSG00000239503 ENSG00000239503 4.45300601599872 4.16126426346173 4.30713513973022 NA
ENSG00000279862 ENSG00000279862 4.15219467913303 4.88198035756045 4.51708751834674 NA
ENSG00000236434 ENSG00000236434 4.22897039377978 4.96204105093882 4.5955057223593 NA
ENSG00000228166 ENSG00000228166 4.4130961908377 5.13609335610494 4.77459477347132 MTND1P11
ENSG00000208028 ENSG00000208028 4.43080090566233 5.14219914778293 4.78650002672263 MIR616
ENSG00000274093 ENSG00000274093 4.46751039995011 5.19686640469241 4.83218840232126 NA
ENSG00000259950 ENSG00000259950 4.47434940757891 5.20193033004558 4.83813986881225 NA
ENSG00000257475 ENSG00000257475 4.49058063961706 5.21053708997933 4.8505588647982 NA
ENSG00000265625 ENSG00000265625 4.51258922011669 5.22035659802475 4.86647290907072 NA
ENSG00000253539 ENSG00000253539 4.66024587128113 5.38117831898838 5.02071209513475 NA
ENSG00000179038 ENSG00000179038 5.09426473364569 5.80355437865827 5.44890955615198 NA
ENSG00000085265 ENSG00000085265 5.41025559710872 6.11905544475849 5.76465552093361 FCN1

Reactome - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

KEGG - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

BP - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

CC - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

MF - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

BP - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0002181 cytoplasmic translation 1.31e-19 NA NA 9.11e-03
GO:0006412 translation 7.01e-10 NA NA 4.71e-02
GO:0045333 cellular respiration 2.79e-07 NA NA NA
GO:0032543 mitochondrial translation 9.03e-07 NA NA NA
GO:0097250 mitochondrial respirasome assembly 2.06e-06 NA NA NA
GO:0140053 mitochondrial gene expression 7.70e-06 NA NA NA
GO:0006119 oxidative phosphorylation 7.70e-06 NA NA NA
GO:0033108 mitochondrial respiratory chain complex ... 7.70e-06 NA NA NA
GO:0009060 aerobic respiration 1.77e-05 NA NA NA
GO:0017004 cytochrome complex assembly 2.00e-05 NA NA NA
GO:0022904 respiratory electron transport chain 5.87e-04 NA NA NA
GO:0007005 mitochondrion organization 1.10e-03 NA NA NA
GO:0046165 alcohol biosynthetic process 1.26e-03 NA NA NA
GO:0015980 energy derivation by oxidation of organi... 1.26e-03 NA NA NA
GO:0097237 cellular response to toxic substance 1.26e-03 NA NA NA
GO:0022900 electron transport chain 1.26e-03 NA NA NA
GO:0042773 ATP synthesis coupled electron transport 1.70e-03 NA NA NA
GO:0042775 mitochondrial ATP synthesis coupled elec... 1.70e-03 NA NA NA
GO:0019646 aerobic electron transport chain 2.20e-03 NA NA NA
GO:0033617 mitochondrial cytochrome c oxidase assem... 2.30e-03 NA NA NA
GO:1990748 cellular detoxification 2.70e-03 NA NA NA
GO:0098754 detoxification 3.09e-03 NA NA NA
GO:0006754 ATP biosynthetic process 3.93e-03 NA NA NA
GO:0019538 protein metabolic process 6.67e-03 NA NA NA
GO:0008535 respiratory chain complex IV assembly 7.45e-03 NA NA NA
GO:0009145 purine nucleoside triphosphate biosynthe... 7.49e-03 NA NA NA
GO:0061077 chaperone-mediated protein folding 7.49e-03 NA NA NA
GO:0015986 proton motive force-driven ATP synthesis 7.49e-03 NA NA NA
GO:0009206 purine ribonucleoside triphosphate biosy... 7.49e-03 NA NA NA
GO:0098869 cellular oxidant detoxification 8.08e-03 NA NA NA
GO:1902600 proton transmembrane transport 8.08e-03 NA NA NA
GO:1901137 carbohydrate derivative biosynthetic pro... 8.08e-03 NA NA 2.69e-02
GO:0006121 mitochondrial electron transport, succin... 8.08e-03 NA NA NA
GO:1901617 organic hydroxy compound biosynthetic pr... 8.09e-03 NA NA NA
GO:0030003 intracellular monoatomic cation homeosta... 8.34e-03 NA NA NA
GO:1902253 regulation of intrinsic apoptotic signal... 8.34e-03 NA NA NA
GO:1901135 carbohydrate derivative metabolic proces... 1.01e-02 NA NA NA
GO:0045116 protein neddylation 1.09e-02 NA NA NA
GO:0006091 generation of precursor metabolites and ... 1.16e-02 NA NA NA
GO:0055086 nucleobase-containing small molecule met... 1.51e-02 NA NA 4.18e-02
GO:0006839 mitochondrial transport 1.68e-02 NA NA NA
GO:0006873 intracellular monoatomic ion homeostasis 1.74e-02 NA NA NA
GO:0006626 protein targeting to mitochondrion 1.74e-02 NA NA NA
GO:0031666 positive regulation of lipopolysaccharid... 1.78e-02 NA NA NA
GO:0006695 cholesterol biosynthetic process 1.86e-02 NA NA NA
GO:1902653 secondary alcohol biosynthetic process 1.86e-02 NA NA NA
GO:0051246 regulation of protein metabolic process 2.08e-02 NA NA NA
GO:0009636 response to toxic substance 2.08e-02 NA NA NA
GO:0046085 adenosine metabolic process 2.62e-02 NA NA NA
GO:0070585 protein localization to mitochondrion 2.75e-02 NA NA NA
GO:0090481 pyrimidine nucleotide-sugar transmembran... 3.13e-02 NA NA NA
GO:0009954 proximal/distal pattern formation 3.15e-02 NA NA NA
GO:1900118 negative regulation of execution phase o... 3.23e-02 NA NA NA
GO:0016126 sterol biosynthetic process 3.26e-02 NA NA NA
GO:0009201 ribonucleoside triphosphate biosynthetic... 3.36e-02 NA NA NA
GO:0006457 protein folding 3.36e-02 NA NA NA
GO:0090151 establishment of protein localization to... 3.36e-02 NA NA NA
GO:0042776 proton motive force-driven mitochondrial... 3.36e-02 NA NA NA
GO:0009117 nucleotide metabolic process 3.36e-02 NA NA NA
GO:0009142 nucleoside triphosphate biosynthetic pro... 3.36e-02 NA NA NA
GO:0006753 nucleoside phosphate metabolic process 3.61e-02 NA NA 4.18e-02
GO:0006694 steroid biosynthetic process 3.61e-02 NA NA NA
GO:1901857 positive regulation of cellular respirat... 3.94e-02 NA NA NA
GO:0030162 regulation of proteolysis 4.30e-02 NA NA NA
GO:0006959 humoral immune response 4.35e-02 NA NA NA
GO:0006163 purine nucleotide metabolic process 4.69e-02 NA NA NA
GO:0072521 purine-containing compound metabolic pro... 4.69e-02 NA NA NA
GO:0030150 protein import into mitochondrial matrix 4.78e-02 NA NA NA
GO:0006325 chromatin organization NA 3.48e-17 NA NA
GO:0006338 chromatin remodeling NA 1.35e-16 NA NA
GO:0016043 cellular component organization NA 3.19e-10 1.73e-03 NA
GO:0071840 cellular component organization or bioge... NA 2.09e-08 4.96e-02 NA
GO:0000226 microtubule cytoskeleton organization NA 1.50e-07 NA NA
GO:0007049 cell cycle NA 2.27e-07 NA NA
GO:0022402 cell cycle process NA 3.30e-07 NA NA
GO:0051254 positive regulation of RNA metabolic pro... NA 4.08e-07 NA NA
GO:0007010 cytoskeleton organization NA 4.08e-07 NA NA
GO:1902680 positive regulation of RNA biosynthetic ... NA 4.08e-07 NA NA
GO:0045935 positive regulation of nucleobase-contai... NA 4.08e-07 NA NA
GO:0010564 regulation of cell cycle process NA 4.16e-07 NA NA
GO:0045893 positive regulation of DNA-templated tra... NA 4.47e-07 NA NA
GO:0019219 regulation of nucleobase-containing comp... NA 7.84e-07 NA NA
GO:2001141 regulation of RNA biosynthetic process NA 8.63e-07 NA NA
GO:0006355 regulation of DNA-templated transcriptio... NA 1.07e-06 NA NA
GO:0051252 regulation of RNA metabolic process NA 1.27e-06 NA NA
GO:0051726 regulation of cell cycle NA 2.00e-06 NA NA
GO:0006366 transcription by RNA polymerase II NA 3.12e-06 NA NA
GO:0006351 DNA-templated transcription NA 4.02e-06 NA NA
GO:0007017 microtubule-based process NA 5.15e-06 NA NA
GO:0090304 nucleic acid metabolic process NA 5.15e-06 NA NA
GO:0000278 mitotic cell cycle NA 5.98e-06 NA NA
GO:0051056 regulation of small GTPase mediated sign... NA 6.22e-06 NA NA
GO:0006357 regulation of transcription by RNA polym... NA 6.22e-06 NA NA
GO:1903047 mitotic cell cycle process NA 6.22e-06 NA NA
GO:0050794 regulation of cellular process NA 1.38e-05 2.33e-02 NA
GO:0016070 RNA metabolic process NA 1.38e-05 NA NA
GO:1902679 negative regulation of RNA biosynthetic ... NA 3.94e-05 NA NA
GO:0045892 negative regulation of DNA-templated tra... NA 4.60e-05 NA NA
GO:0050789 regulation of biological process NA 4.69e-05 1.54e-02 NA
GO:0051276 chromosome organization NA 4.69e-05 NA NA
GO:0045934 negative regulation of nucleobase-contai... NA 4.92e-05 NA NA
GO:0000122 negative regulation of transcription by ... NA 9.04e-05 NA NA
GO:0032774 RNA biosynthetic process NA 9.20e-05 NA NA
GO:0045944 positive regulation of transcription by ... NA 1.15e-04 NA NA
GO:0141187 nucleic acid biosynthetic process NA 1.15e-04 NA NA
GO:0065007 biological regulation NA 1.86e-04 3.35e-03 NA
GO:0046777 protein autophosphorylation NA 3.24e-04 NA NA
GO:0006974 DNA damage response NA 3.54e-04 NA NA
GO:0000819 sister chromatid segregation NA 4.55e-04 NA NA
GO:0030261 chromosome condensation NA 4.58e-04 NA NA
GO:0051253 negative regulation of RNA metabolic pro... NA 4.87e-04 NA NA
GO:0140014 mitotic nuclear division NA 7.77e-04 NA NA
GO:0006281 DNA repair NA 8.58e-04 NA NA
GO:0098534 centriole assembly NA 1.04e-03 NA NA
GO:0032886 regulation of microtubule-based process NA 1.05e-03 NA NA
GO:0051128 regulation of cellular component organiz... NA 1.05e-03 2.01e-02 NA
GO:0048856 anatomical structure development NA 1.14e-03 NA NA
GO:0071716 leukotriene transport NA 1.21e-03 NA NA
GO:0010468 regulation of gene expression NA 1.40e-03 NA NA
GO:0031023 microtubule organizing center organizati... NA 1.59e-03 NA NA
GO:0051301 cell division NA 1.66e-03 NA NA
GO:0007098 centrosome cycle NA 1.70e-03 NA NA
GO:0007275 multicellular organism development NA 1.80e-03 NA NA
GO:1905064 negative regulation of vascular associat... NA 1.82e-03 NA NA
GO:0010556 regulation of macromolecule biosynthetic... NA 1.96e-03 NA NA
GO:0016310 phosphorylation NA 2.06e-03 NA NA
GO:0040029 epigenetic regulation of gene expression NA 2.06e-03 NA NA
GO:0031326 regulation of cellular biosynthetic proc... NA 2.24e-03 NA NA
GO:0051052 regulation of DNA metabolic process NA 2.31e-03 NA NA
GO:0007059 chromosome segregation NA 2.92e-03 NA NA
GO:0000070 mitotic sister chromatid segregation NA 3.39e-03 NA NA
GO:0022008 neurogenesis NA 3.56e-03 4.65e-02 NA
GO:0006139 nucleobase-containing compound metabolic... NA 3.65e-03 NA NA
GO:0000280 nuclear division NA 3.86e-03 NA NA
GO:0007264 small GTPase-mediated signal transductio... NA 3.86e-03 NA NA
GO:0033044 regulation of chromosome organization NA 3.96e-03 NA NA
GO:0048731 system development NA 3.96e-03 NA NA
GO:0034654 nucleobase-containing compound biosynthe... NA 3.96e-03 NA NA
GO:0098813 nuclear chromosome segregation NA 4.08e-03 NA NA
GO:0034983 peptidyl-lysine deacetylation NA 4.09e-03 NA NA
GO:0051716 cellular response to stimulus NA 4.09e-03 NA NA
GO:1901987 regulation of cell cycle phase transitio... NA 4.24e-03 NA NA
GO:0000022 mitotic spindle elongation NA 4.24e-03 NA NA
GO:0007399 nervous system development NA 4.39e-03 NA NA
GO:0031327 negative regulation of cellular biosynth... NA 4.46e-03 NA NA
GO:0031111 negative regulation of microtubule polym... NA 4.61e-03 NA NA
GO:0009889 regulation of biosynthetic process NA 4.74e-03 NA NA
GO:0007099 centriole replication NA 4.74e-03 NA NA
GO:0007346 regulation of mitotic cell cycle NA 4.89e-03 NA NA
GO:0033043 regulation of organelle organization NA 5.02e-03 NA NA
GO:0048699 generation of neurons NA 5.05e-03 3.63e-02 NA
GO:0006259 DNA metabolic process NA 5.05e-03 NA NA
GO:0009888 tissue development NA 5.22e-03 NA NA
GO:0010558 negative regulation of macromolecule bio... NA 5.24e-03 NA NA
GO:0048513 animal organ development NA 5.89e-03 NA NA
GO:0032502 developmental process NA 5.97e-03 NA NA
GO:0031109 microtubule polymerization or depolymeri... NA 5.99e-03 NA NA
GO:0007052 mitotic spindle organization NA 6.17e-03 NA NA
GO:0009890 negative regulation of biosynthetic proc... NA 6.40e-03 NA NA
GO:0030030 cell projection organization NA 6.83e-03 3.35e-03 NA
GO:0006282 regulation of DNA repair NA 7.32e-03 NA NA
GO:0031324 negative regulation of cellular metaboli... NA 7.32e-03 NA NA
GO:0051987 positive regulation of attachment of spi... NA 7.43e-03 NA NA
GO:0006468 protein phosphorylation NA 8.42e-03 NA NA
GO:0051983 regulation of chromosome segregation NA 9.10e-03 NA NA
GO:0051256 mitotic spindle midzone assembly NA 9.18e-03 NA NA
GO:1902275 regulation of chromatin organization NA 9.99e-03 NA NA
GO:2000779 regulation of double-strand break repair NA 9.99e-03 NA NA
GO:0048869 cellular developmental process NA 1.07e-02 NA NA
GO:1902850 microtubule cytoskeleton organization in... NA 1.19e-02 NA NA
GO:0030154 cell differentiation NA 1.19e-02 NA NA
GO:0032501 multicellular organismal process NA 1.23e-02 NA NA
GO:0048468 cell development NA 1.33e-02 NA NA
GO:0007026 negative regulation of microtubule depol... NA 1.33e-02 NA NA
GO:0044770 cell cycle phase transition NA 1.35e-02 NA NA
GO:0045814 negative regulation of gene expression, ... NA 1.36e-02 NA NA
GO:0002295 T-helper cell lineage commitment NA 1.54e-02 NA NA
GO:0034244 negative regulation of transcription elo... NA 1.70e-02 NA NA
GO:0006996 organelle organization NA 1.70e-02 1.67e-02 NA
GO:0051298 centrosome duplication NA 2.14e-02 NA NA
GO:1901990 regulation of mitotic cell cycle phase t... NA 2.18e-02 NA NA
GO:0021999 neural plate anterior/posterior regional... NA 2.21e-02 NA NA
GO:0051054 positive regulation of DNA metabolic pro... NA 2.21e-02 NA NA
GO:0070507 regulation of microtubule cytoskeleton o... NA 2.26e-02 NA NA
GO:0031331 positive regulation of cellular cataboli... NA 2.26e-02 NA NA
GO:0035556 intracellular signal transduction NA 2.26e-02 NA NA
GO:0034728 nucleosome organization NA 2.33e-02 NA NA
GO:0045721 negative regulation of gluconeogenesis NA 2.42e-02 NA NA
GO:0120036 plasma membrane bounded cell projection ... NA 2.42e-02 2.24e-03 NA
GO:0009653 anatomical structure morphogenesis NA 2.54e-02 NA NA
GO:0010172 embryonic body morphogenesis NA 2.56e-02 NA NA
GO:0006302 double-strand break repair NA 2.60e-02 NA NA
GO:0043087 regulation of GTPase activity NA 2.63e-02 NA NA
GO:0048812 neuron projection morphogenesis NA 2.69e-02 NA NA
GO:0021915 neural tube development NA 2.69e-02 NA NA
GO:1904781 positive regulation of protein localizat... NA 2.69e-02 NA NA
GO:0030182 neuron differentiation NA 2.69e-02 NA NA
GO:0007019 microtubule depolymerization NA 2.69e-02 NA NA
GO:0010557 positive regulation of macromolecule bio... NA 2.69e-02 NA NA
GO:0031328 positive regulation of cellular biosynth... NA 2.69e-02 NA NA
GO:0032785 negative regulation of DNA-templated tra... NA 3.00e-02 NA 4.71e-02
GO:2000781 positive regulation of double-strand bre... NA 3.00e-02 NA NA
GO:0031573 mitotic intra-S DNA damage checkpoint si... NA 3.07e-02 NA NA
GO:0007088 regulation of mitotic nuclear division NA 3.08e-02 NA NA
GO:0051782 negative regulation of cell division NA 3.23e-02 NA NA
GO:0031445 regulation of heterochromatin formation NA 3.31e-02 NA NA
GO:0045786 negative regulation of cell cycle NA 3.39e-02 NA NA
GO:0000281 mitotic cytokinesis NA 3.43e-02 NA NA
GO:0120039 plasma membrane bounded cell projection ... NA 3.43e-02 NA NA
GO:0050896 response to stimulus NA 3.45e-02 NA NA
GO:0046785 microtubule polymerization NA 3.52e-02 NA NA
GO:0009891 positive regulation of biosynthetic proc... NA 3.53e-02 NA NA
GO:0090068 positive regulation of cell cycle proces... NA 3.56e-02 NA NA
GO:0031048 regulatory ncRNA-mediated heterochromati... NA 3.56e-02 NA NA
GO:0048858 cell projection morphogenesis NA 3.56e-02 NA NA
GO:1903939 regulation of TORC2 signaling NA 3.58e-02 NA NA
GO:0010948 negative regulation of cell cycle proces... NA 3.60e-02 NA NA
GO:0030263 apoptotic chromosome condensation NA 3.60e-02 NA NA
GO:2001251 negative regulation of chromosome organi... NA 3.68e-02 NA NA
GO:0072540 T-helper 17 cell lineage commitment NA 3.71e-02 NA NA
GO:0010457 centriole-centriole cohesion NA 3.84e-02 NA NA
GO:0048285 organelle fission NA 3.98e-02 NA NA
GO:0010720 positive regulation of cell development NA 4.00e-02 NA NA
GO:0051231 spindle elongation NA 4.00e-02 NA NA
GO:0044380 protein localization to cytoskeleton NA 4.03e-02 NA NA
GO:0050772 positive regulation of axonogenesis NA 4.11e-02 NA NA
GO:0006884 cell volume homeostasis NA 4.15e-02 NA NA
GO:0030866 cortical actin cytoskeleton organization NA 4.31e-02 NA NA
GO:0048522 positive regulation of cellular process NA 4.31e-02 NA NA
GO:0033045 regulation of sister chromatid segregati... NA 4.34e-02 NA NA
GO:0031110 regulation of microtubule polymerization... NA 4.96e-02 NA NA
GO:0048518 positive regulation of biological proces... NA 4.96e-02 NA NA
GO:0036289 peptidyl-serine autophosphorylation NA 5.00e-02 NA NA
GO:0016192 vesicle-mediated transport NA NA 1.96e-05 NA
GO:0051641 cellular localization NA NA 1.28e-03 NA
GO:0051649 establishment of localization in cell NA NA 1.73e-03 NA
GO:0033036 macromolecule localization NA NA 1.74e-03 NA
GO:0044088 regulation of vacuole organization NA NA 1.74e-03 NA
GO:0070727 cellular macromolecule localization NA NA 2.24e-03 NA
GO:0008104 protein localization NA NA 2.66e-03 NA
GO:0046907 intracellular transport NA NA 3.19e-03 NA
GO:0007033 vacuole organization NA NA 3.35e-03 NA
GO:0015031 protein transport NA NA 4.42e-03 NA
GO:0016197 endosomal transport NA NA 5.99e-03 NA
GO:1903944 negative regulation of hepatocyte apopto... NA NA 6.29e-03 NA
GO:0010743 regulation of macrophage derived foam ce... NA NA 6.38e-03 NA
GO:0046348 amino sugar catabolic process NA NA 7.10e-03 NA
GO:0016050 vesicle organization NA NA 7.10e-03 NA
GO:0045184 establishment of protein localization NA NA 1.12e-02 NA
GO:0051130 positive regulation of cellular componen... NA NA 1.12e-02 NA
GO:0006886 intracellular protein transport NA NA 1.14e-02 NA
GO:0060271 cilium assembly NA NA 1.14e-02 NA
GO:1903943 regulation of hepatocyte apoptotic proce... NA NA 1.28e-02 NA
GO:2000785 regulation of autophagosome assembly NA NA 1.54e-02 NA
GO:0044782 cilium organization NA NA 1.54e-02 NA
GO:0120031 plasma membrane bounded cell projection ... NA NA 2.01e-02 NA
GO:0007030 Golgi organization NA NA 2.01e-02 NA
GO:0051179 localization NA NA 2.01e-02 NA
GO:0030031 cell projection assembly NA NA 2.08e-02 NA
GO:0019953 sexual reproduction NA NA 2.33e-02 NA
GO:0070925 organelle assembly NA NA 2.36e-02 NA
GO:0048609 multicellular organismal reproductive pr... NA NA 2.44e-02 NA
GO:0071705 nitrogen compound transport NA NA 2.44e-02 NA
GO:1905515 non-motile cilium assembly NA NA 2.49e-02 NA
GO:0007034 vacuolar transport NA NA 2.49e-02 NA
GO:0044248 cellular catabolic process NA NA 2.49e-02 NA
GO:0010745 negative regulation of macrophage derive... NA NA 2.49e-02 NA
GO:0048193 Golgi vesicle transport NA NA 3.21e-02 NA
GO:0007276 gamete generation NA NA 3.26e-02 NA
GO:0010256 endomembrane system organization NA NA 3.31e-02 NA
GO:0007626 locomotory behavior NA NA 3.38e-02 NA
GO:0072001 renal system development NA NA 3.70e-02 NA
GO:0007040 lysosome organization NA NA 3.70e-02 NA
GO:0080171 lytic vacuole organization NA NA 3.70e-02 NA
GO:0048666 neuron development NA NA 3.70e-02 NA
GO:0046856 phosphatidylinositol dephosphorylation NA NA 3.80e-02 NA
GO:0019262 N-acetylneuraminate catabolic process NA NA 3.90e-02 NA
GO:0002092 positive regulation of receptor internal... NA NA 3.90e-02 NA
GO:0006897 endocytosis NA NA 3.93e-02 NA
GO:0051129 negative regulation of cellular componen... NA NA 4.79e-02 NA
GO:1901072 glucosamine-containing compound cataboli... NA NA 4.96e-02 NA
GO:0021694 cerebellar Purkinje cell layer formation NA NA 4.96e-02 NA
GO:0042254 ribosome biogenesis NA NA NA 3.59e-05
GO:0016072 rRNA metabolic process NA NA NA 4.08e-05
GO:0006364 rRNA processing NA NA NA 3.53e-04
GO:0000727 double-strand break repair via break-ind... NA NA NA 1.14e-03
GO:0022613 ribonucleoprotein complex biogenesis NA NA NA 1.35e-03
GO:0042274 ribosomal small subunit biogenesis NA NA NA 1.68e-02
GO:0006560 proline metabolic process NA NA NA 2.25e-02
GO:0010155 regulation of proton transport NA NA NA 2.69e-02
GO:0006561 proline biosynthetic process NA NA NA 2.69e-02
GO:0055129 L-proline biosynthetic process NA NA NA 2.69e-02
GO:0006735 NADH regeneration NA NA NA 2.69e-02
GO:0061621 canonical glycolysis NA NA NA 2.69e-02
GO:0061718 glucose catabolic process to pyruvate NA NA NA 2.69e-02
GO:0072527 pyrimidine-containing compound metabolic... NA NA NA 3.02e-02
GO:0061620 glycolytic process through glucose-6-pho... NA NA NA 3.02e-02
GO:0006271 DNA strand elongation involved in DNA re... NA NA NA 3.35e-02
GO:0006399 tRNA metabolic process NA NA NA 4.18e-02
GO:0044283 small molecule biosynthetic process NA NA NA 4.18e-02
GO:0009141 nucleoside triphosphate metabolic proces... NA NA NA 4.18e-02
GO:0009260 ribonucleotide biosynthetic process NA NA NA 4.18e-02
GO:0044281 small molecule metabolic process NA NA NA 4.60e-02
GO:0042273 ribosomal large subunit biogenesis NA NA NA 4.62e-02
GO:0090329 regulation of DNA-templated DNA replicat... NA NA NA 4.71e-02
GO:1901293 nucleoside phosphate biosynthetic proces... NA NA NA 4.71e-02
GO:0046390 ribose phosphate biosynthetic process NA NA NA 4.71e-02
GO:0006220 pyrimidine nucleotide metabolic process NA NA NA 4.71e-02
GO:0032075 positive regulation of nuclease activity NA NA NA 4.91e-02
GO:0009199 ribonucleoside triphosphate metabolic pr... NA NA NA 4.91e-02
GO:0009220 pyrimidine ribonucleotide biosynthetic p... NA NA NA 4.92e-02
GO:0006261 DNA-templated DNA replication NA NA NA 4.92e-02

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0006338 chromatin remodeling NA 5.57e-04 NA
GO:0006325 chromatin organization NA 2.82e-03 NA
GO:0032785 negative regulation of DNA-templated tra... NA 7.12e-03 NA
GO:0034244 negative regulation of transcription elo... NA 8.80e-03 NA
GO:0000122 negative regulation of transcription by ... NA 8.99e-03 NA
GO:0045892 negative regulation of DNA-templated tra... NA 2.06e-02 NA
GO:0000727 double-strand break repair via break-ind... NA 2.35e-02 NA
GO:0000022 mitotic spindle elongation NA 2.35e-02 NA
GO:1902679 negative regulation of RNA biosynthetic ... NA 2.35e-02 NA
GO:0045934 negative regulation of nucleobase-contai... NA 3.40e-02 NA
GO:0006261 DNA-templated DNA replication NA 4.03e-02 NA

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0031347 regulation of defense response 7.47e-14 NA NA NA
GO:0080134 regulation of response to stress 7.47e-14 NA NA NA
GO:0010608 post-transcriptional regulation of gene ... 8.13e-14 NA NA NA
GO:0009894 regulation of catabolic process 1.15e-13 NA NA NA
GO:0000278 mitotic cell cycle 2.42e-13 NA NA NA
GO:1903047 mitotic cell cycle process 2.42e-13 NA NA NA
GO:0007049 cell cycle 2.53e-13 NA NA NA
GO:0022402 cell cycle process 2.53e-13 NA NA NA
GO:0031399 regulation of protein modification proce... 4.62e-13 NA NA NA
GO:0044770 cell cycle phase transition 4.62e-13 NA NA NA
GO:0051276 chromosome organization 5.99e-13 NA NA NA
GO:0051052 regulation of DNA metabolic process 8.23e-13 NA NA NA
GO:0006974 DNA damage response 8.77e-13 NA NA NA
GO:0009057 macromolecule catabolic process 9.28e-13 NA NA NA
GO:0006259 DNA metabolic process 9.28e-13 NA NA NA
GO:0030163 protein catabolic process 5.44e-12 NA NA NA
GO:0032787 monocarboxylic acid metabolic process 9.56e-12 NA NA NA
GO:0140546 defense response to symbiont 2.02e-08 NA NA NA
GO:0045087 innate immune response 6.50e-08 NA NA NA
GO:0009889 regulation of biosynthetic process 1.05e-06 NA NA NA
GO:0031326 regulation of cellular biosynthetic proc... 1.05e-06 NA NA NA
GO:0031323 regulation of cellular metabolic process 1.08e-06 NA NA NA
GO:0019222 regulation of metabolic process 1.46e-06 NA NA NA
GO:0090304 nucleic acid metabolic process 2.74e-06 NA NA NA
GO:0060255 regulation of macromolecule metabolic pr... 3.33e-06 NA NA NA
GO:0010468 regulation of gene expression 8.46e-06 NA NA NA
GO:0010556 regulation of macromolecule biosynthetic... 8.46e-06 NA NA NA
GO:0044249 cellular biosynthetic process 9.39e-06 NA NA NA
GO:0080090 regulation of primary metabolic process 2.18e-05 NA NA NA
GO:0016070 RNA metabolic process 2.30e-05 NA NA NA
GO:0032774 RNA biosynthetic process 2.30e-05 NA NA NA
GO:0141187 nucleic acid biosynthetic process 2.30e-05 NA NA NA
GO:0009059 macromolecule biosynthetic process 6.10e-05 NA NA NA
GO:0010467 gene expression 6.10e-05 NA NA NA
GO:0043170 macromolecule metabolic process 1.26e-04 NA NA NA
GO:0019219 regulation of nucleobase-containing comp... 2.29e-04 NA NA NA
GO:0051252 regulation of RNA metabolic process 7.73e-04 NA NA NA
GO:0010604 positive regulation of macromolecule met... 7.90e-04 NA NA NA
GO:0009893 positive regulation of metabolic process 8.77e-04 NA NA NA
GO:0009891 positive regulation of biosynthetic proc... 1.84e-03 NA NA NA
GO:0031328 positive regulation of cellular biosynth... 1.84e-03 NA NA NA
GO:0006351 DNA-templated transcription 2.46e-03 NA NA NA
GO:0050794 regulation of cellular process 2.62e-03 NA NA NA
GO:0050789 regulation of biological process 3.21e-03 NA NA NA
GO:0031325 positive regulation of cellular metaboli... 3.98e-03 NA NA NA
GO:0031324 negative regulation of cellular metaboli... 4.59e-03 NA NA NA
GO:0006355 regulation of DNA-templated transcriptio... 5.95e-03 NA NA NA
GO:2001141 regulation of RNA biosynthetic process 5.95e-03 NA NA NA
GO:0010557 positive regulation of macromolecule bio... 9.75e-03 NA NA NA
GO:0043412 macromolecule modification 1.21e-02 NA NA NA
GO:0048518 positive regulation of biological proces... 1.35e-02 NA NA NA
GO:0006357 regulation of transcription by RNA polym... 1.39e-02 NA NA NA
GO:0006366 transcription by RNA polymerase II 1.39e-02 NA NA NA
GO:0048523 negative regulation of cellular process 1.52e-02 NA NA NA
GO:0048519 negative regulation of biological proces... 1.53e-02 NA NA NA
GO:0045184 establishment of protein localization 1.86e-02 NA NA NA
GO:0065007 biological regulation 2.24e-02 NA NA NA
GO:0048585 negative regulation of response to stimu... 2.24e-02 NA NA NA
GO:0036211 protein modification process 2.42e-02 NA NA NA
GO:0045935 positive regulation of nucleobase-contai... 2.46e-02 NA NA NA
GO:0009890 negative regulation of biosynthetic proc... 2.46e-02 NA NA NA
GO:0010558 negative regulation of macromolecule bio... 2.46e-02 NA NA NA
GO:0031327 negative regulation of cellular biosynth... 2.46e-02 NA NA NA
GO:0048522 positive regulation of cellular process 3.18e-02 NA NA NA
GO:0009892 negative regulation of metabolic process 3.21e-02 NA NA NA
GO:0051246 regulation of protein metabolic process 3.25e-02 NA NA NA
GO:0009056 catabolic process 3.25e-02 NA NA NA
GO:0015031 protein transport 3.93e-02 NA NA NA
GO:0008219 cell death 4.03e-02 NA NA NA
GO:0012501 programmed cell death 4.03e-02 NA NA NA
GO:0033036 macromolecule localization 4.03e-02 NA NA NA
GO:0033554 cellular response to stress 4.12e-02 NA NA NA
GO:0009968 negative regulation of signal transducti... 4.60e-02 NA NA NA
GO:0009058 biosynthetic process 4.80e-02 NA NA NA
GO:0051254 positive regulation of RNA metabolic pro... 4.80e-02 NA NA NA
GO:0070482 response to oxygen levels NA 1.82e-21 2.01e-03 NA
GO:0001666 response to hypoxia NA 1.82e-21 7.07e-03 NA
GO:0036293 response to decreased oxygen levels NA 1.82e-21 7.07e-03 NA
GO:0006164 purine nucleotide biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:0006754 ATP biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:0009142 nucleoside triphosphate biosynthetic pro... NA 1.82e-21 6.92e-08 NA
GO:0009145 purine nucleoside triphosphate biosynthe... NA 1.82e-21 6.92e-08 NA
GO:0009152 purine ribonucleotide biosynthetic proce... NA 1.82e-21 6.92e-08 NA
GO:0009165 nucleotide biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:0009201 ribonucleoside triphosphate biosynthetic... NA 1.82e-21 6.92e-08 NA
GO:0009206 purine ribonucleoside triphosphate biosy... NA 1.82e-21 6.92e-08 NA
GO:0009260 ribonucleotide biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:0015986 proton motive force-driven ATP synthesis NA 1.82e-21 6.92e-08 NA
GO:0042776 proton motive force-driven mitochondrial... NA 1.82e-21 6.92e-08 NA
GO:0046390 ribose phosphate biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:0072522 purine-containing compound biosynthetic ... NA 1.82e-21 6.92e-08 NA
GO:0090407 organophosphate biosynthetic process NA 1.82e-21 6.92e-08 NA
GO:1901137 carbohydrate derivative biosynthetic pro... NA 1.82e-21 6.92e-08 NA
GO:1901293 nucleoside phosphate biosynthetic proces... NA 1.82e-21 6.92e-08 NA
GO:0010257 NADH dehydrogenase complex assembly NA 4.45e-21 3.84e-14 NA
GO:0032981 mitochondrial respiratory chain complex ... NA 4.45e-21 3.84e-14 NA
GO:0006120 mitochondrial electron transport, NADH t... NA 4.45e-21 1.60e-14 NA
GO:0009060 aerobic respiration NA 7.72e-08 3.44e-08 NA
GO:0015980 energy derivation by oxidation of organi... NA 7.72e-08 3.44e-08 NA
GO:0045333 cellular respiration NA 7.72e-08 3.44e-08 NA
GO:0006119 oxidative phosphorylation NA 6.00e-07 6.92e-08 NA
GO:0022900 electron transport chain NA 4.04e-06 3.41e-04 NA
GO:1902600 proton transmembrane transport NA 4.04e-06 2.05e-07 NA
GO:0019646 aerobic electron transport chain NA 2.26e-05 6.92e-08 NA
GO:0022904 respiratory electron transport chain NA 2.26e-05 6.92e-08 NA
GO:0042773 ATP synthesis coupled electron transport NA 2.26e-05 6.92e-08 NA
GO:0042775 mitochondrial ATP synthesis coupled elec... NA 2.26e-05 6.92e-08 NA
GO:0098660 inorganic ion transmembrane transport NA 3.80e-05 NA NA
GO:0098662 inorganic cation transmembrane transport NA 3.80e-05 NA NA
GO:0006091 generation of precursor metabolites and ... NA 1.26e-04 2.76e-04 NA
GO:0006811 monoatomic ion transport NA 1.96e-04 NA NA
GO:0006812 monoatomic cation transport NA 1.96e-04 NA NA
GO:0034220 monoatomic ion transmembrane transport NA 5.62e-04 NA NA
GO:0098655 monoatomic cation transmembrane transpor... NA 5.62e-04 NA NA
GO:0055085 transmembrane transport NA 3.66e-03 NA NA
GO:0006163 purine nucleotide metabolic process NA 7.57e-03 1.00e-02 NA
GO:0006753 nucleoside phosphate metabolic process NA 7.57e-03 1.00e-02 NA
GO:0009117 nucleotide metabolic process NA 7.57e-03 1.00e-02 NA
GO:0009141 nucleoside triphosphate metabolic proces... NA 7.57e-03 1.00e-02 NA
GO:0009144 purine nucleoside triphosphate metabolic... NA 7.57e-03 1.00e-02 NA
GO:0009150 purine ribonucleotide metabolic process NA 7.57e-03 1.00e-02 NA
GO:0009199 ribonucleoside triphosphate metabolic pr... NA 7.57e-03 1.00e-02 NA
GO:0009205 purine ribonucleoside triphosphate metab... NA 7.57e-03 1.00e-02 NA
GO:0009259 ribonucleotide metabolic process NA 7.57e-03 1.00e-02 NA
GO:0019637 organophosphate metabolic process NA 7.57e-03 1.00e-02 NA
GO:0019693 ribose phosphate metabolic process NA 7.57e-03 1.00e-02 NA
GO:0046034 ATP metabolic process NA 7.57e-03 1.00e-02 NA
GO:0055086 nucleobase-containing small molecule met... NA 7.57e-03 1.00e-02 NA
GO:0072521 purine-containing compound metabolic pro... NA 7.57e-03 1.00e-02 NA
GO:1901135 carbohydrate derivative metabolic proces... NA 7.57e-03 1.00e-02 NA
GO:0014070 response to organic cyclic compound NA 1.51e-02 NA NA
GO:0033108 mitochondrial respiratory chain complex ... NA NA 3.72e-14 NA
GO:0097250 mitochondrial respirasome assembly NA NA 3.72e-14 NA
GO:0043933 protein-containing complex organization NA NA 9.67e-03 NA
GO:0065003 protein-containing complex assembly NA NA 1.29e-02 NA

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
NA NA NA NA NA

CC - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0044391 ribosomal subunit 1.32e-41 NA NA 6.64e-05
GO:0022625 cytosolic large ribosomal subunit 5.84e-32 NA NA 6.75e-05
GO:0005840 ribosome 1.05e-27 NA NA 1.09e-03
GO:0022626 cytosolic ribosome 2.36e-26 NA NA 1.87e-02
GO:0015934 large ribosomal subunit 6.61e-25 NA NA 6.75e-05
GO:0043230 extracellular organelle 3.76e-23 NA NA NA
GO:0065010 extracellular membrane-bounded organelle 3.76e-23 NA NA NA
GO:0070062 extracellular exosome 3.76e-23 NA NA NA
GO:1903561 extracellular vesicle 4.60e-23 NA NA NA
GO:0022627 cytosolic small ribosomal subunit 1.41e-18 NA NA NA
GO:0005615 extracellular space 1.41e-18 NA NA NA
GO:0005576 extracellular region 1.85e-18 NA NA NA
GO:0015935 small ribosomal subunit 1.35e-17 NA NA NA
GO:0005743 mitochondrial inner membrane 1.13e-15 NA NA 8.74e-06
GO:0005740 mitochondrial envelope 2.94e-15 NA NA 4.30e-04
GO:0019866 organelle inner membrane 3.21e-15 NA NA 8.74e-06
GO:0031966 mitochondrial membrane 1.57e-14 NA NA 1.79e-03
GO:0031090 organelle membrane 3.51e-13 NA NA NA
GO:0031982 vesicle 3.00e-11 NA NA NA
GO:0005739 mitochondrion 3.54e-11 NA NA 4.30e-05
GO:0005783 endoplasmic reticulum 1.14e-09 NA NA NA
GO:0098798 mitochondrial protein-containing complex 1.42e-09 NA NA 4.52e-03
GO:0031967 organelle envelope 3.21e-09 NA NA 1.63e-02
GO:1990904 ribonucleoprotein complex 3.38e-08 NA NA 3.05e-04
GO:0030141 secretory granule 6.45e-08 NA NA NA
GO:0098796 membrane protein complex 1.14e-07 NA NA NA
GO:0000313 organellar ribosome 1.14e-07 NA NA NA
GO:0005761 mitochondrial ribosome 1.14e-07 NA NA NA
GO:0042175 nuclear outer membrane-endoplasmic retic... 2.60e-07 NA NA NA
GO:0005789 endoplasmic reticulum membrane 2.79e-07 NA NA NA
GO:0098827 endoplasmic reticulum subcompartment 3.38e-07 NA NA NA
GO:0005925 focal adhesion 8.59e-07 NA NA 2.57e-02
GO:0030055 cell-substrate junction 1.32e-06 NA NA 2.66e-02
GO:0099503 secretory vesicle 2.26e-06 NA NA NA
GO:0000315 organellar large ribosomal subunit 5.37e-06 NA NA NA
GO:0005762 mitochondrial large ribosomal subunit 5.37e-06 NA NA NA
GO:0005759 mitochondrial matrix 5.42e-06 NA NA 1.09e-03
GO:0012505 endomembrane system 1.05e-05 NA NA NA
GO:0098803 respiratory chain complex 1.27e-05 NA NA NA
GO:0035577 azurophil granule membrane 4.07e-05 NA NA NA
GO:0016020 membrane 1.12e-04 NA NA NA
GO:1990351 transporter complex 1.30e-04 NA NA NA
GO:0030667 secretory granule membrane 1.70e-04 NA NA NA
GO:0005766 primary lysosome 1.77e-04 NA NA NA
GO:0042582 azurophil granule 1.77e-04 NA NA NA
GO:0031984 organelle subcompartment 2.76e-04 NA NA NA
GO:0000314 organellar small ribosomal subunit 4.87e-04 NA NA NA
GO:0005763 mitochondrial small ribosomal subunit 4.87e-04 NA NA NA
GO:0098556 cytoplasmic side of rough endoplasmic re... 7.10e-04 NA NA NA
GO:1902495 transmembrane transporter complex 7.39e-04 NA NA NA
GO:0042470 melanosome 7.76e-04 NA NA NA
GO:0048770 pigment granule 7.76e-04 NA NA NA
GO:0016469 proton-transporting two-sector ATPase co... 9.24e-04 NA NA NA
GO:0140534 endoplasmic reticulum protein-containing... 9.26e-04 NA NA NA
GO:0005758 mitochondrial intermembrane space 1.00e-03 NA NA NA
GO:0030662 coated vesicle membrane 1.17e-03 NA NA NA
GO:1905369 endopeptidase complex 1.23e-03 NA NA NA
GO:0098588 bounding membrane of organelle 1.50e-03 NA NA NA
GO:0005688 U6 snRNP 1.53e-03 NA NA NA
GO:0097197 tetraspanin-enriched microdomain 1.58e-03 NA NA NA
GO:0030135 coated vesicle 2.00e-03 NA NA NA
GO:0042719 mitochondrial intermembrane space protei... 2.06e-03 NA NA NA
GO:0043227 membrane-bounded organelle 2.46e-03 NA NA NA
GO:0005885 Arp2/3 protein complex 2.46e-03 NA NA NA
GO:0101002 ficolin-1-rich granule 2.56e-03 NA NA NA
GO:0031983 vesicle lumen 2.63e-03 NA NA NA
GO:0060205 cytoplasmic vesicle lumen 2.63e-03 NA NA NA
GO:0030659 cytoplasmic vesicle membrane 2.81e-03 NA 4.84e-02 NA
GO:0000502 proteasome complex 3.57e-03 NA NA NA
GO:0098857 membrane microdomain 3.65e-03 NA NA NA
GO:0030670 phagocytic vesicle membrane 3.91e-03 NA NA NA
GO:0034774 secretory granule lumen 3.93e-03 NA NA NA
GO:0012506 vesicle membrane 4.04e-03 NA NA NA
GO:0045261 proton-transporting ATP synthase complex... 4.07e-03 NA NA NA
GO:0120115 Lsm2-8 complex 4.10e-03 NA NA NA
GO:1904813 ficolin-1-rich granule lumen 4.15e-03 NA NA NA
GO:0005787 signal peptidase complex 4.30e-03 NA NA NA
GO:1990204 oxidoreductase complex 4.30e-03 NA NA NA
GO:0070820 tertiary granule 4.34e-03 NA NA NA
GO:0005683 U7 snRNP 4.65e-03 NA NA NA
GO:0140596 TOM complex 5.40e-03 NA NA NA
GO:0045121 membrane raft 5.92e-03 NA NA NA
GO:0031410 cytoplasmic vesicle 6.45e-03 NA NA NA
GO:0005834 heterotrimeric G-protein complex 6.79e-03 NA NA NA
GO:0031970 organelle envelope lumen 7.05e-03 NA NA NA
GO:0071204 histone pre-mRNA 3'end processing comple... 8.39e-03 NA NA NA
GO:0030134 COPII-coated ER to Golgi transport vesic... 8.48e-03 NA NA NA
GO:0097708 intracellular vesicle 8.50e-03 NA 4.84e-02 NA
GO:0030666 endocytic vesicle membrane 9.81e-03 NA NA NA
GO:0090533 cation-transporting ATPase complex 1.46e-02 NA NA NA
GO:0045259 proton-transporting ATP synthase complex 1.57e-02 NA NA NA
GO:1905368 peptidase complex 1.66e-02 NA NA NA
GO:0030665 clathrin-coated vesicle membrane 1.68e-02 NA NA NA
GO:0001405 PAM complex, Tim23 associated import mot... 1.70e-02 NA NA NA
GO:0043231 intracellular membrane-bounded organelle 1.87e-02 NA NA NA
GO:0005839 proteasome core complex 1.87e-02 NA NA NA
GO:0009986 cell surface 2.01e-02 NA NA NA
GO:0008250 oligosaccharyltransferase complex 2.09e-02 NA NA NA
GO:0033178 proton-transporting two-sector ATPase co... 2.53e-02 NA NA NA
GO:1905360 GTPase complex 2.54e-02 NA NA NA
GO:0030133 transport vesicle 2.64e-02 NA 2.81e-02 NA
GO:0005744 TIM23 mitochondrial import inner membran... 2.65e-02 NA NA 2.57e-02
GO:0005838 proteasome regulatory particle 3.10e-02 NA NA NA
GO:0005791 rough endoplasmic reticulum 3.39e-02 NA NA NA
GO:0043505 CENP-A containing nucleosome 3.60e-02 NA NA NA
GO:0061638 CENP-A containing chromatin 3.60e-02 NA NA NA
GO:0036126 sperm flagellum 3.60e-02 NA NA NA
GO:0072546 EMC complex 3.63e-02 NA NA NA
GO:0005765 lysosomal membrane 3.63e-02 NA 4.63e-03 NA
GO:0098852 lytic vacuole membrane 3.63e-02 NA 4.63e-03 NA
GO:0098800 inner mitochondrial membrane protein com... 3.63e-02 NA NA 1.02e-02
GO:0097729 9+2 motile cilium 3.69e-02 NA NA NA
GO:0034715 pICln-Sm protein complex 3.78e-02 NA NA NA
GO:0098552 side of membrane 3.80e-02 NA NA NA
GO:0032991 protein-containing complex 4.02e-02 NA NA NA
GO:0034709 methylosome 4.46e-02 NA NA NA
GO:0005774 vacuolar membrane 4.46e-02 NA 1.76e-03 NA
GO:0030136 clathrin-coated vesicle 4.47e-02 NA NA NA
GO:0062023 collagen-containing extracellular matrix 4.72e-02 NA NA NA
GO:0045335 phagocytic vesicle 4.96e-02 NA NA NA
GO:0070821 tertiary granule membrane 4.96e-02 NA NA NA
GO:0005694 chromosome NA 2.88e-11 NA NA
GO:0005856 cytoskeleton NA 7.38e-10 NA NA
GO:0000785 chromatin NA 9.21e-10 NA NA
GO:0015630 microtubule cytoskeleton NA 4.77e-09 NA NA
GO:0043228 non-membrane-bounded organelle NA 3.22e-08 NA NA
GO:0043232 intracellular non-membrane-bounded organ... NA 3.22e-08 NA NA
GO:0005815 microtubule organizing center NA 2.82e-07 2.03e-02 NA
GO:0005814 centriole NA 3.53e-07 NA NA
GO:0005654 nucleoplasm NA 1.26e-05 NA NA
GO:0005813 centrosome NA 3.83e-05 1.76e-03 NA
GO:0016604 nuclear body NA 1.23e-04 2.96e-03 NA
GO:0031981 nuclear lumen NA 2.28e-04 NA NA
GO:0016607 nuclear speck NA 5.03e-04 NA NA
GO:0035097 histone methyltransferase complex NA 1.54e-03 NA NA
GO:0005634 nucleus NA 2.56e-03 NA NA
GO:0000922 spindle pole NA 2.60e-03 NA NA
GO:0099512 supramolecular fiber NA 3.14e-03 NA NA
GO:0099081 supramolecular polymer NA 3.56e-03 NA NA
GO:0034451 centriolar satellite NA 4.76e-03 NA NA
GO:0140513 nuclear protein-containing complex NA 4.76e-03 NA NA
GO:0034399 nuclear periphery NA 5.98e-03 NA NA
GO:0005819 spindle NA 7.58e-03 NA NA
GO:0005874 microtubule NA 7.58e-03 NA NA
GO:0032437 cuticular plate NA 7.58e-03 NA NA
GO:0099513 polymeric cytoskeletal fiber NA 8.33e-03 NA NA
GO:0036064 ciliary basal body NA 8.81e-03 NA NA
GO:0035976 transcription factor AP-1 complex NA 1.21e-02 NA NA
GO:0016363 nuclear matrix NA 1.21e-02 NA NA
GO:0099080 supramolecular complex NA 1.32e-02 NA NA
GO:0070603 SWI/SNF superfamily-type complex NA 1.65e-02 NA NA
GO:0044665 MLL1/2 complex NA 1.79e-02 NA NA
GO:0031931 TORC1 complex NA 1.99e-02 NA NA
GO:0042995 cell projection NA 2.62e-02 NA NA
GO:0005871 kinesin complex NA 2.65e-02 NA NA
GO:0005859 muscle myosin complex NA 2.65e-02 NA NA
GO:0035371 microtubule plus-end NA 2.65e-02 NA NA
GO:0014731 spectrin-associated cytoskeleton NA 2.70e-02 NA NA
GO:0000347 THO complex NA 2.70e-02 NA NA
GO:0000445 THO complex part of transcription export... NA 2.70e-02 NA NA
GO:0048786 presynaptic active zone NA 2.70e-02 NA NA
GO:0071339 MLL1 complex NA 2.70e-02 NA NA
GO:1990752 microtubule end NA 2.92e-02 NA NA
GO:0070776 MOZ/MORF histone acetyltransferase compl... NA 3.39e-02 NA NA
GO:0090543 Flemming body NA 3.39e-02 NA NA
GO:0120025 plasma membrane bounded cell projection NA 3.39e-02 NA NA
GO:0070775 H3 histone acetyltransferase complex NA 3.85e-02 NA NA
GO:0099023 vesicle tethering complex NA 3.85e-02 NA NA
GO:0030686 90S preribosome NA 3.85e-02 NA NA
GO:0005622 intracellular anatomical structure NA 4.72e-02 4.84e-02 NA
GO:0005770 late endosome NA NA 3.22e-05 NA
GO:0005768 endosome NA NA 1.16e-04 NA
GO:0005773 vacuole NA NA 1.80e-04 NA
GO:0000323 lytic vacuole NA NA 4.65e-04 NA
GO:0005764 lysosome NA NA 4.65e-04 NA
GO:0005769 early endosome NA NA 5.28e-04 NA
GO:0010008 endosome membrane NA NA 8.85e-04 NA
GO:0005802 trans-Golgi network NA NA 1.05e-03 NA
GO:0031902 late endosome membrane NA NA 1.65e-03 NA
GO:0031901 early endosome membrane NA NA 2.53e-03 NA
GO:0098791 Golgi apparatus subcompartment NA NA 1.06e-02 NA
GO:0000776 kinetochore NA NA 2.87e-02 NA
GO:0098793 presynapse NA NA 3.70e-02 NA
GO:0008021 synaptic vesicle NA NA 4.79e-02 NA
GO:0000779 condensed chromosome, centromeric region NA NA 4.84e-02 NA
GO:0042827 platelet dense granule NA NA 4.84e-02 NA
GO:0005942 phosphatidylinositol 3-kinase complex NA NA 4.84e-02 NA
GO:0005829 cytosol NA NA 4.84e-02 NA
GO:0071162 CMG complex NA NA NA 1.79e-03
GO:0030684 preribosome NA NA NA 2.08e-03
GO:0031261 DNA replication preinitiation complex NA NA NA 3.63e-03
GO:0032040 small-subunit processome NA NA NA 1.02e-02
GO:0031390 Ctf18 RFC-like complex NA NA NA 1.18e-02
GO:0001725 stress fiber NA NA NA 2.51e-02
GO:0097517 contractile actin filament bundle NA NA NA 2.51e-02
GO:0043527 tRNA methyltransferase complex NA NA NA 3.48e-02
GO:0032432 actin filament bundle NA NA NA 4.02e-02

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0099503 secretory vesicle 5.22e-03 NA NA
GO:0030893 meiotic cohesin complex 2.95e-02 NA NA
GO:0098793 presynapse 2.95e-02 NA NA
GO:0031983 vesicle lumen 2.95e-02 NA NA
GO:0060205 cytoplasmic vesicle lumen 2.95e-02 NA NA
GO:0034774 secretory granule lumen 2.97e-02 NA NA
GO:0005694 chromosome NA 5.60e-03 NA
GO:0000785 chromatin NA 9.75e-03 NA
GO:0043228 non-membrane-bounded organelle NA 9.75e-03 NA
GO:0043232 intracellular non-membrane-bounded organ... NA 9.75e-03 NA
GO:0031094 platelet dense tubular network NA 3.98e-02 NA
GO:0031095 platelet dense tubular network membrane NA 3.98e-02 NA
GO:0140513 nuclear protein-containing complex NA 3.98e-02 NA
GO:0030686 90S preribosome NA 3.98e-02 NA
GO:0031931 TORC1 complex NA 3.98e-02 NA
GO:0005654 nucleoplasm NA 3.98e-02 NA
GO:0005856 cytoskeleton NA 3.98e-02 NA
GO:1903561 extracellular vesicle NA NA 3.72e-03
GO:0043230 extracellular organelle NA NA 3.72e-03
GO:0065010 extracellular membrane-bounded organelle NA NA 3.72e-03
GO:0044391 ribosomal subunit NA NA 3.97e-03
GO:0070062 extracellular exosome NA NA 4.46e-03
GO:0031982 vesicle NA NA 8.56e-03
GO:0030135 coated vesicle NA NA 3.55e-02
GO:0030662 coated vesicle membrane NA NA 4.61e-02
GO:0005802 trans-Golgi network NA NA 4.83e-02
GO:0071204 histone pre-mRNA 3'end processing comple... NA NA 4.83e-02

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0000139 Golgi membrane 2.08e-13 NA NA NA
GO:0048471 perinuclear region of cytoplasm 1.45e-12 NA NA NA
GO:0000228 nuclear chromosome 1.45e-12 NA NA NA
GO:0005634 nucleus 3.23e-04 NA NA NA
GO:0031981 nuclear lumen 1.99e-03 NA NA NA
GO:0005654 nucleoplasm 4.34e-02 NA NA NA
GO:0031974 membrane-enclosed lumen 4.34e-02 NA NA NA
GO:0043233 organelle lumen 4.34e-02 NA NA NA
GO:0070013 intracellular organelle lumen 4.34e-02 NA NA NA
GO:0030964 NADH dehydrogenase complex NA 9.39e-22 7.82e-15 NA
GO:0045271 respiratory chain complex I NA 9.39e-22 7.82e-15 NA
GO:0110165 cellular anatomical entity NA 3.63e-13 1.32e-02 NA
GO:1902495 transmembrane transporter complex NA 6.58e-07 2.58e-04 NA
GO:1990351 transporter complex NA 6.58e-07 2.58e-04 NA
GO:0098803 respiratory chain complex NA 4.08e-06 2.33e-07 NA
GO:1990204 oxidoreductase complex NA 2.09e-05 1.19e-07 NA
GO:0098796 membrane protein complex NA 2.09e-05 1.80e-03 NA
GO:0005743 mitochondrial inner membrane NA 6.92e-05 8.76e-09 NA
GO:0031966 mitochondrial membrane NA 2.50e-04 2.54e-08 NA
GO:0019866 organelle inner membrane NA 8.14e-04 1.12e-07 NA
GO:0005740 mitochondrial envelope NA 1.45e-03 9.24e-07 NA
GO:0005739 mitochondrion NA 2.60e-03 2.27e-06 NA
GO:0031090 organelle membrane NA 4.49e-03 NA NA
GO:0031967 organelle envelope NA 1.14e-02 7.56e-07 NA
GO:0016020 membrane NA 1.75e-02 NA NA
GO:1902494 catalytic complex NA NA 2.31e-03 NA
GO:0070069 cytochrome complex NA NA 2.79e-02 NA

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0098588 bounding membrane of organelle 1.29e-02 NA NA
GO:0000228 nuclear chromosome 1.29e-02 NA NA
GO:0005765 lysosomal membrane 1.61e-02 NA NA
GO:0005774 vacuolar membrane 1.61e-02 NA NA
GO:0098852 lytic vacuole membrane 1.61e-02 NA NA

MF - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0003735 structural constituent of ribosome 6.65e-39 NA NA 1.11e-05
GO:0019843 rRNA binding 5.24e-07 NA NA NA
GO:0005198 structural molecule activity 3.84e-06 NA NA NA
GO:0003924 GTPase activity 6.98e-05 NA NA NA
GO:0009055 electron transfer activity 1.17e-04 NA NA NA
GO:0005525 GTP binding 6.35e-04 NA NA NA
GO:0019001 guanyl nucleotide binding 6.35e-04 NA NA NA
GO:0032561 guanyl ribonucleotide binding 6.35e-04 NA NA NA
GO:0003925 G protein activity 1.09e-03 NA NA NA
GO:0097177 mitochondrial ribosome binding 1.11e-03 NA NA NA
GO:0015038 glutathione disulfide oxidoreductase act... 1.11e-03 NA NA NA
GO:0016491 oxidoreductase activity 1.11e-03 NA NA NA
GO:0019003 GDP binding 1.68e-03 NA NA NA
GO:0016209 antioxidant activity 1.86e-03 NA NA NA
GO:0008430 selenium binding 3.91e-03 NA NA NA
GO:0016684 oxidoreductase activity, acting on perox... 6.32e-03 NA NA NA
GO:0004601 peroxidase activity 1.07e-02 NA NA NA
GO:0015078 proton transmembrane transporter activit... 1.86e-02 NA NA NA
GO:0032977 membrane insertase activity 2.40e-02 NA NA NA
GO:0097371 MDM2/MDM4 family protein binding 2.42e-02 NA NA NA
GO:1903136 cuprous ion binding 2.49e-02 NA NA NA
GO:0004930 G protein-coupled receptor activity 2.96e-02 NA NA NA
GO:0061650 ubiquitin-like protein conjugating enzym... 3.08e-02 NA NA NA
GO:0019763 immunoglobulin receptor activity 3.08e-02 NA NA NA
GO:0044183 protein folding chaperone 3.30e-02 NA NA NA
GO:0015165 pyrimidine nucleotide-sugar transmembran... 3.30e-02 NA NA NA
GO:0051920 peroxiredoxin activity 3.30e-02 NA NA NA
GO:0031386 protein tag activity 3.30e-02 NA NA NA
GO:0141047 molecular tag activity 3.30e-02 NA NA NA
GO:0019864 IgG binding 4.27e-02 NA NA NA
GO:0015288 porin activity 4.35e-02 NA NA NA
GO:0005524 ATP binding NA 1.22e-19 NA NA
GO:0032559 adenyl ribonucleotide binding NA 1.87e-19 NA NA
GO:0030554 adenyl nucleotide binding NA 4.11e-17 NA NA
GO:0030695 GTPase regulator activity NA 2.63e-16 NA NA
GO:0060589 nucleoside-triphosphatase regulator acti... NA 2.63e-16 NA NA
GO:0005096 GTPase activator activity NA 5.02e-13 NA NA
GO:0140993 histone modifying activity NA 8.55e-12 NA NA
GO:0004672 protein kinase activity NA 2.21e-11 NA NA
GO:0016773 phosphotransferase activity, alcohol gro... NA 6.19e-11 NA NA
GO:0042393 histone binding NA 6.28e-11 NA NA
GO:0003682 chromatin binding NA 1.15e-10 NA NA
GO:0016301 kinase activity NA 1.47e-10 NA NA
GO:0106310 protein serine kinase activity NA 5.81e-10 NA NA
GO:0004674 protein serine/threonine kinase activity NA 8.07e-10 NA NA
GO:0043167 ion binding NA 3.06e-09 NA NA
GO:0035639 purine ribonucleoside triphosphate bindi... NA 3.88e-09 NA NA
GO:0032553 ribonucleotide binding NA 5.87e-09 NA NA
GO:0032555 purine ribonucleotide binding NA 6.68e-09 NA NA
GO:0043168 anion binding NA 9.32e-09 NA NA
GO:0016887 ATP hydrolysis activity NA 9.47e-09 NA NA
GO:0016772 transferase activity, transferring phosp... NA 2.07e-08 NA NA
GO:0005085 guanyl-nucleotide exchange factor activi... NA 8.40e-08 NA NA
GO:0017076 purine nucleotide binding NA 1.05e-07 NA NA
GO:0140657 ATP-dependent activity NA 2.04e-07 NA NA
GO:0003677 DNA binding NA 2.41e-07 NA NA
GO:0036094 small molecule binding NA 6.65e-07 NA NA
GO:1901363 heterocyclic compound binding NA 1.16e-06 NA NA
GO:1901265 nucleoside phosphate binding NA 1.85e-06 NA NA
GO:0140030 modification-dependent protein binding NA 1.85e-06 NA NA
GO:0000166 nucleotide binding NA 2.21e-06 NA NA
GO:0004386 helicase activity NA 5.21e-06 NA NA
GO:0035173 histone kinase activity NA 1.18e-05 NA NA
GO:0097367 carbohydrate derivative binding NA 1.23e-05 NA NA
GO:0140457 protein demethylase activity NA 1.40e-05 2.90e-02 NA
GO:0044024 histone H2AS1 kinase activity NA 1.63e-05 NA NA
GO:0140995 histone H2A kinase activity NA 1.63e-05 NA NA
GO:0140096 catalytic activity, acting on a protein NA 1.77e-05 NA NA
GO:0008017 microtubule binding NA 1.92e-05 NA NA
GO:0031267 small GTPase binding NA 1.92e-05 1.18e-02 NA
GO:0032452 histone demethylase activity NA 2.34e-05 4.26e-02 NA
GO:0035091 phosphatidylinositol binding NA 7.44e-05 NA NA
GO:0046872 metal ion binding NA 7.59e-05 1.79e-02 NA
GO:0003712 transcription coregulator activity NA 9.64e-05 NA NA
GO:0141052 histone H3 demethylase activity NA 1.12e-04 1.46e-02 NA
GO:0051020 GTPase binding NA 1.18e-04 1.79e-02 NA
GO:0015631 tubulin binding NA 1.47e-04 NA NA
GO:0043169 cation binding NA 2.07e-04 1.79e-02 NA
GO:0035064 methylated histone binding NA 3.08e-04 NA NA
GO:0140110 transcription regulator activity NA 3.35e-04 NA NA
GO:0008047 enzyme activator activity NA 5.56e-04 NA NA
GO:0008381 mechanosensitive monoatomic ion channel ... NA 6.40e-04 NA NA
GO:0032451 demethylase activity NA 6.40e-04 NA NA
GO:0140034 methylation-dependent protein binding NA 6.40e-04 NA NA
GO:0003916 DNA topoisomerase activity NA 6.78e-04 NA NA
GO:0140947 histone H3K9me2 methyltransferase activi... NA 8.69e-04 NA NA
GO:0030674 protein-macromolecule adaptor activity NA 8.72e-04 NA NA
GO:0097159 organic cyclic compound binding NA 1.01e-03 NA NA
GO:0016706 2-oxoglutarate-dependent dioxygenase act... NA 1.04e-03 NA NA
GO:0043565 sequence-specific DNA binding NA 1.10e-03 NA NA
GO:0005516 calmodulin binding NA 1.35e-03 NA NA
GO:0140999 histone H3K4 trimethyltransferase activi... NA 1.42e-03 NA NA
GO:0071889 14-3-3 protein binding NA 1.42e-03 NA NA
GO:0140359 ABC-type transporter activity NA 1.72e-03 NA NA
GO:0003774 cytoskeletal motor activity NA 1.74e-03 NA NA
GO:0008092 cytoskeletal protein binding NA 1.74e-03 NA NA
GO:0140658 ATP-dependent chromatin remodeler activi... NA 1.86e-03 NA NA
GO:0140033 acetylation-dependent protein binding NA 2.17e-03 NA NA
GO:0140097 catalytic activity, acting on DNA NA 2.51e-03 NA NA
GO:0016740 transferase activity NA 2.56e-03 NA NA
GO:0005078 MAP-kinase scaffold activity NA 2.85e-03 NA NA
GO:0060090 molecular adaptor activity NA 3.10e-03 NA NA
GO:0004713 protein tyrosine kinase activity NA 3.10e-03 NA NA
GO:0008443 phosphofructokinase activity NA 3.17e-03 NA NA
GO:0140938 histone H3 methyltransferase activity NA 3.33e-03 NA NA
GO:0003713 transcription coactivator activity NA 3.36e-03 NA NA
GO:0140640 catalytic activity, acting on a nucleic ... NA 3.36e-03 NA NA
GO:0070577 lysine-acetylated histone binding NA 3.94e-03 NA NA
GO:0003777 microtubule motor activity NA 4.20e-03 NA NA
GO:0010484 histone H3 acetyltransferase activity NA 4.77e-03 NA NA
GO:0005543 phospholipid binding NA 5.13e-03 NA NA
GO:0008094 ATP-dependent activity, acting on DNA NA 5.16e-03 NA NA
GO:0008289 lipid binding NA 6.52e-03 NA NA
GO:0008186 ATP-dependent activity, acting on RNA NA 6.89e-03 NA NA
GO:0030234 enzyme regulator activity NA 7.12e-03 NA NA
GO:0046976 histone H3K27 methyltransferase activity NA 8.56e-03 NA NA
GO:0141039 phosphatidylinositol 3-kinase inhibitor ... NA 9.05e-03 NA NA
GO:0008349 MAP kinase kinase kinase kinase activity NA 9.89e-03 NA NA
GO:0034040 ATPase-coupled lipid transmembrane trans... NA 1.09e-02 NA NA
GO:0003690 double-stranded DNA binding NA 1.09e-02 NA NA
GO:1904680 peptide transmembrane transporter activi... NA 1.20e-02 NA NA
GO:0051864 histone H3K36 demethylase activity NA 1.27e-02 NA NA
GO:0008134 transcription factor binding NA 1.33e-02 NA NA
GO:0004016 adenylate cyclase activity NA 1.33e-02 NA NA
GO:0003724 RNA helicase activity NA 1.36e-02 NA NA
GO:0016741 transferase activity, transferring one-c... NA 1.37e-02 NA NA
GO:0015278 intracellularly gated calcium channel ac... NA 1.37e-02 NA NA
GO:1990837 sequence-specific double-stranded DNA bi... NA 1.48e-02 NA NA
GO:0042054 histone methyltransferase activity NA 1.54e-02 NA NA
GO:0042162 telomeric DNA binding NA 1.56e-02 NA NA
GO:0046030 inositol trisphosphate phosphatase activ... NA 1.59e-02 NA NA
GO:0140939 histone H4 methyltransferase activity NA 1.59e-02 NA NA
GO:0004709 MAP kinase kinase kinase activity NA 1.64e-02 NA NA
GO:0005272 sodium channel activity NA 1.69e-02 NA NA
GO:0022836 gated channel activity NA 1.69e-02 NA NA
GO:0034647 histone H3K4me/H3K4me2/H3K4me3 demethyla... NA 1.71e-02 NA NA
GO:0052659 inositol-1,3,4,5-tetrakisphosphate 5-pho... NA 1.72e-02 NA NA
GO:0051213 dioxygenase activity NA 1.82e-02 NA NA
GO:0008559 ABC-type xenobiotic transporter activity NA 1.88e-02 NA NA
GO:0000976 transcription cis-regulatory region bind... NA 2.08e-02 NA NA
GO:0004812 aminoacyl-tRNA ligase activity NA 2.09e-02 NA NA
GO:0016875 ligase activity, forming carbon-oxygen b... NA 2.09e-02 NA NA
GO:0001067 transcription regulatory region nucleic ... NA 2.13e-02 NA NA
GO:0008168 methyltransferase activity NA 2.48e-02 NA NA
GO:0003714 transcription corepressor activity NA 2.71e-02 NA NA
GO:0043225 ATPase-coupled inorganic anion transmemb... NA 2.76e-02 NA NA
GO:0099604 ligand-gated calcium channel activity NA 3.06e-02 NA NA
GO:0008170 N-methyltransferase activity NA 3.39e-02 NA NA
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate... NA 3.73e-02 NA NA
GO:0050681 nuclear androgen receptor binding NA 3.75e-02 NA NA
GO:0001227 DNA-binding transcription repressor acti... NA 3.75e-02 NA NA
GO:0015081 sodium ion transmembrane transporter act... NA 3.81e-02 NA NA
GO:0043995 histone H4K5 acetyltransferase activity NA 3.90e-02 NA NA
GO:0043996 histone H4K8 acetyltransferase activity NA 3.90e-02 NA NA
GO:0042887 amide transmembrane transporter activity NA 4.02e-02 NA NA
GO:0022834 ligand-gated channel activity NA 4.03e-02 NA NA
GO:0016849 phosphorus-oxygen lyase activity NA 4.14e-02 NA NA
GO:1990841 promoter-specific chromatin binding NA 4.29e-02 NA NA
GO:0016278 lysine N-methyltransferase activity NA 4.29e-02 NA NA
GO:0016279 protein-lysine N-methyltransferase activ... NA 4.29e-02 NA NA
GO:0008574 plus-end-directed microtubule motor acti... NA 4.32e-02 NA NA
GO:1901981 phosphatidylinositol phosphate binding NA 4.32e-02 NA NA
GO:0015431 ABC-type glutathione S-conjugate transpo... NA 4.32e-02 NA NA
GO:0015923 mannosidase activity NA 4.32e-02 NA NA
GO:0004559 alpha-mannosidase activity NA 4.32e-02 NA NA
GO:0008276 protein methyltransferase activity NA 4.32e-02 NA NA
GO:0005217 intracellularly ligand-gated monoatomic ... NA 4.32e-02 NA NA
GO:0001217 DNA-binding transcription repressor acti... NA 4.38e-02 NA NA
GO:0140297 DNA-binding transcription factor binding NA 4.41e-02 NA NA
GO:0019901 protein kinase binding NA 4.43e-02 NA NA
GO:0140566 histone reader activity NA 4.43e-02 NA NA
GO:0003950 NAD+-protein poly-ADP-ribosyltransferase... NA 4.78e-02 NA NA
GO:0015276 ligand-gated monoatomic ion channel acti... NA 4.82e-02 NA NA
GO:0090482 vitamin transmembrane transporter activi... NA 4.85e-02 NA NA
GO:0046914 transition metal ion binding NA NA 1.03e-02 NA
GO:0000149 SNARE binding NA NA 1.03e-02 NA
GO:0008270 zinc ion binding NA NA 1.22e-02 NA
GO:0043394 proteoglycan binding NA NA 1.46e-02 NA
GO:0019783 ubiquitin-like protein peptidase activit... NA NA 1.79e-02 NA
GO:0032454 histone H3K9 demethylase activity NA NA 2.90e-02 NA
GO:0004843 cysteine-type deubiquitinase activity NA NA 3.91e-02 NA
GO:0101005 deubiquitinase activity NA NA 4.00e-02 NA
GO:0005488 binding NA NA 4.34e-02 NA

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0070728 L-leucine binding 4.31e-02 NA NA
GO:0005524 ATP binding NA 9.02e-08 NA
GO:0032559 adenyl ribonucleotide binding NA 9.02e-08 NA
GO:0030554 adenyl nucleotide binding NA 1.45e-07 NA
GO:0035639 purine ribonucleoside triphosphate bindi... NA 1.58e-04 NA
GO:0140993 histone modifying activity NA 1.58e-04 NA
GO:0032553 ribonucleotide binding NA 1.64e-04 NA
GO:0032555 purine ribonucleotide binding NA 1.70e-04 NA
GO:1901363 heterocyclic compound binding NA 2.56e-04 NA
GO:0017076 purine nucleotide binding NA 2.56e-04 NA
GO:0016773 phosphotransferase activity, alcohol gro... NA 2.65e-04 NA
GO:1901265 nucleoside phosphate binding NA 3.74e-04 NA
GO:0016301 kinase activity NA 3.74e-04 NA
GO:0000166 nucleotide binding NA 3.82e-04 NA
GO:0106310 protein serine kinase activity NA 4.62e-04 NA
GO:0043168 anion binding NA 4.62e-04 NA
GO:0004674 protein serine/threonine kinase activity NA 5.32e-04 NA
GO:0003682 chromatin binding NA 6.57e-04 NA
GO:0004672 protein kinase activity NA 6.57e-04 NA
GO:0030695 GTPase regulator activity NA 2.45e-03 NA
GO:0060589 nucleoside-triphosphatase regulator acti... NA 2.45e-03 NA
GO:0016772 transferase activity, transferring phosp... NA 2.70e-03 NA
GO:0035242 protein-arginine omega-N asymmetric meth... NA 4.95e-03 NA
GO:0097367 carbohydrate derivative binding NA 5.33e-03 NA
GO:0016741 transferase activity, transferring one-c... NA 5.82e-03 NA
GO:0008168 methyltransferase activity NA 7.95e-03 NA
GO:0042393 histone binding NA 1.13e-02 NA
GO:0008381 mechanosensitive monoatomic ion channel ... NA 1.20e-02 NA
GO:0071889 14-3-3 protein binding NA 1.92e-02 NA
GO:0003714 transcription corepressor activity NA 2.19e-02 NA
GO:0097159 organic cyclic compound binding NA 2.25e-02 NA
GO:0005096 GTPase activator activity NA 2.25e-02 NA
GO:0001217 DNA-binding transcription repressor acti... NA 2.25e-02 NA
GO:0003712 transcription coregulator activity NA 2.25e-02 NA
GO:0016887 ATP hydrolysis activity NA 2.30e-02 NA
GO:0140416 transcription regulator inhibitor activi... NA 2.34e-02 NA
GO:0035173 histone kinase activity NA 2.44e-02 NA
GO:0001227 DNA-binding transcription repressor acti... NA 2.52e-02 NA
GO:0008276 protein methyltransferase activity NA 3.28e-02 NA
GO:0042054 histone methyltransferase activity NA 3.82e-02 NA
GO:0140030 modification-dependent protein binding NA 4.56e-02 NA
GO:0017020 myosin phosphatase regulator activity NA 4.77e-02 NA
GO:0008757 S-adenosylmethionine-dependent methyltra... NA 4.94e-02 NA
GO:0003735 structural constituent of ribosome NA NA 7.54e-03

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0005488 binding 2.00e-17 NA NA NA
GO:0008270 zinc ion binding 1.21e-13 NA NA NA
GO:0030674 protein-macromolecule adaptor activity 6.64e-13 NA NA NA
GO:0000977 RNA polymerase II transcription regulato... 7.40e-10 NA NA NA
GO:0003723 RNA binding 7.59e-03 NA NA NA
GO:0003677 DNA binding 2.82e-02 NA NA NA
GO:0008137 NADH dehydrogenase (ubiquinone) activity NA 2.34e-21 1.92e-15 NA
GO:0016651 oxidoreductase activity, acting on NAD(P... NA 2.34e-21 1.92e-15 NA
GO:0016655 oxidoreductase activity, acting on NAD(P... NA 2.34e-21 1.92e-15 NA
GO:0015078 proton transmembrane transporter activit... NA 7.88e-07 6.22e-08 NA
GO:0008324 monoatomic cation transmembrane transpor... NA 6.30e-06 2.79e-02 NA
GO:0015075 monoatomic ion transmembrane transporter... NA 6.30e-06 2.79e-02 NA
GO:0015318 inorganic molecular entity transmembrane... NA 6.30e-06 2.79e-02 NA
GO:0022857 transmembrane transporter activity NA 6.30e-06 2.79e-02 NA
GO:0022890 inorganic cation transmembrane transport... NA 6.30e-06 2.79e-02 NA
GO:0009055 electron transfer activity NA 1.26e-05 6.22e-08 NA
GO:0015399 primary active transmembrane transporter... NA 1.26e-05 6.22e-08 NA
GO:0015453 oxidoreduction-driven active transmembra... NA 1.26e-05 6.22e-08 NA
GO:0005215 transporter activity NA 1.18e-04 3.84e-02 NA
GO:0022804 active transmembrane transporter activit... NA 2.87e-04 2.79e-02 NA
GO:0022853 active monoatomic ion transmembrane tran... NA 2.87e-04 2.79e-02 NA
GO:0016491 oxidoreductase activity NA 9.38e-03 NA NA

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0030674 protein-macromolecule adaptor activity 2.13e-02 NA NA
GO:0060090 molecular adaptor activity 2.13e-02 NA NA

Values of options passed to the Functional Hunter main function

First column contains the option names; second column contains the given values for each option. Note that large data objects (e.g. expression results, organism table and custom annotation files) are not shown.
final_main_params
model_organism Human
annot_table NULL
input_gene_id ENSEMBL
custom NULL
enrich_dbs c("Reactome", "KEGG", "BP", "CC", "MF")
kegg_data_file /Users/marmtnez/Desktop/Master_Bioinfo/TFM/installed_software/ExpHunterSuite/inst/scripts/../../inst/kegg_data_files/hsa_KEGG.rds
enrich_methods ORA
annotation_source orgdb
pthreshold 0.1
qthreshold 0.2
cores 1
task_size 10
output_files /Users/marmtnez/Desktop/Master_Bioinfo/TFM/Results/functional/ctrl_vs_opg_fc1_fe
fc_colname mean_logFCs
universe NULL
clean_parentals FALSE
simplify FALSE
top_categories 50
sim_thr NULL
summary_common_name ancestor
clusters_flag TRUE